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X-RAY DIFFRACTION
Materials and Methods page
3NV2
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8.5
    Temperature 293.0
    Details 20% PEG MME 2000, 0.1M Tris pH 8.5, 0.01M nickel chloride hexahydrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 70.81 α = 90
    b = 70.81 β = 90
    c = 50.21 γ = 120
     
    Space Group
    Space Group Name:    P 63
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 210r
    Collection Date 2009-11-28
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type PHOTON FACTORY BEAMLINE AR-NW12A
    Wavelength List 1.0
    Site PHOTON FACTORY
    Beamline AR-NW12A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.34
    Resolution(Low) 50
    Number Reflections(Observed) 6135
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.075
    B(Isotropic) From Wilson Plot 24.1
    Redundancy 11.2
     
    High Resolution Shell Details
    Resolution(High) 2.34
    Resolution(Low) 2.38
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.385
    Mean I Over Sigma(Observed) 7.4
    Redundancy 11.2
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.34
    Resolution(Low) 38.85
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 5989
    Number of Reflections(Observed) 5989
    Number of Reflections(R-Free) 659
    Percent Reflections(Observed) 97.5
    R-Factor(All) 0.185
    R-Factor(Observed) 0.179
    R-Work 0.179
    R-Free 0.231
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Anisotropic B[1][1] 1.56
    Anisotropic B[1][2] 2.79
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 1.56
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -3.12
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.34
    Shell Resolution(Low) 2.49
    Number of Reflections(Observed) 829
    Number of Reflections(R-Free) 108
    Number of Reflections(R-Work) 829
    R-Factor(R-Work) 0.171
    R-Factor(R-Free) 0.256
    R-Free Error 0.025
    Percent Reflections(Observed) 92.8
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_improper_angle_d 0.76
    c_dihedral_angle_d 27.2
    c_angle_deg 1.5
    c_bond_d 0.005
     
    Coordinate Error
    Luzzati ESD(Observed) 0.21
    Luzzati Sigma A(Observed) 0.12
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.3
    Luzzati Sigma A(R-Free Set) 0.25
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1090
    Nucleic Acid Atoms 0
    Heterogen Atoms 27
    Solvent Atoms 140
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution Molrep
    Structure Refinement CNS 1.1
     
    Software
    refinement CNS version: 1.1
    model building Molrep
    data collection ADSC version: Quantum